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Quality control of single amino acid variations detected by tandem mass spectrometry
Yi, Xinpei1,3; Wang, Bo2; An, Zhiwu1,3; Gong, Fuzhou1,3; Li, Jing2; Fu, Yan1,3
2018-09-15
发表期刊JOURNAL OF PROTEOMICS
ISSN1874-3919
卷号187页码:144-151
摘要Study of single amino acid variations (SAVs) of proteins, resulting from single nucleotide polymorphisms, is of great importance for understanding the relationships between genotype and phenotype. In mass spectrometry based shotgun proteomics, identification of peptides with SAVs often suffers from high error rates on the variant sites detected. These site errors are due to multiple reasons and can be confirmed by manual inspection or genomic sequencing. Here, we present a software tool, named SAVControl, for site-level quality control of variant peptide identifications. It mainly includes strict false discovery rate control of variant peptide identifications and variant site verification by unrestrictive mass shift relocalization. SAVControl was validated on three colorectal adenocarcinoma cell line datasets with genomic sequencing evidences and tested on a colorectal cancer dataset from The Cancer Genome Atlas. The results show that SAVControl can effectively remove false detections of SAVs. Significance: Protein sequence variations caused by single nucleotide polymorphisms (SNPs) are single amino acid variations (SAVs). The investigation of SAVs may provide a chance for understanding the relationships between genotype and phenotype. Mass spectrometry (MS) based proteomics provides a large-scale way to detect SAVs. However, using the current analysis strategy to detect SAVs may lead to high rate of false positives. The SAVControl we present here is a computational workflow and software tool for site-level quality control of SAVs detected by MS. It accesses the confidence of detected variant sites by relocating the mass shift responsible for an SAV to search for alternative interpretations. In addition, it uses a strict false discovery rate control method for variant peptide identifications. The advantages of SAVControl were demonstrated on three colorectal adenocarcinoma cell line datasets and a colorectal cancer dataset. We believe that SAVControl will be a powerful tool for computational proteomics and proteogenomics.
关键词Single amino acid variations Mass spectrometry Peptide identification False discovery rate Unrestrictive mass shift relocalization
DOI10.1016/j.jprot.2018.07.004
语种英语
资助项目Strategic Priority Research Program of CAS[XDB13040600] ; National Natural Science Foundation of China[31271416] ; National Key Basic Research Program of China[2015CB554406] ; Natural Science Foundation of Shanghai[17ZR1413900] ; International S&T Cooperation Program of China[2014DFB30010] ; NCMIS CAS
WOS研究方向Biochemistry & Molecular Biology
WOS类目Biochemical Research Methods
WOS记录号WOS:000444789800013
出版者ELSEVIER SCIENCE BV
引用统计
文献类型期刊论文
条目标识符http://ir.amss.ac.cn/handle/2S8OKBNM/31289
专题应用数学研究所
通讯作者Gong, Fuzhou; Li, Jing; Fu, Yan
作者单位1.Chinese Acad Sci, Acad Math & Syst Sci, RCSDS, NCMIS, Beijing 100190, Peoples R China
2.Shanghai Jiao Tong Univ, Sch Life Sci & Biotechnol, Dept Bioinformat & Biostat, Shanghai 200240, Peoples R China
3.Univ Chinese Acad Sci, Sch Math Sci, Beijing 100049, Peoples R China
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GB/T 7714
Yi, Xinpei,Wang, Bo,An, Zhiwu,et al. Quality control of single amino acid variations detected by tandem mass spectrometry[J]. JOURNAL OF PROTEOMICS,2018,187:144-151.
APA Yi, Xinpei,Wang, Bo,An, Zhiwu,Gong, Fuzhou,Li, Jing,&Fu, Yan.(2018).Quality control of single amino acid variations detected by tandem mass spectrometry.JOURNAL OF PROTEOMICS,187,144-151.
MLA Yi, Xinpei,et al."Quality control of single amino acid variations detected by tandem mass spectrometry".JOURNAL OF PROTEOMICS 187(2018):144-151.
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